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Old 03-22-2017, 05:43 AM   #3
Senior Member
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245

As mentioned, the BAM files you download were prepared and uploaded by the submitter (FASTQ, while supported, is not a preferred format for SRA and is accepted as reference sequences for the aligned read files). So, if you read their methods and are happy with their QC cutoffs and mapping approach, you could use their BAM files. If not, you need to get the actual read files and do your own reference mapping.

Also take note of how old any submission is and what reference release they used. You may want to re-align the reads to a more recent reference build anyway.

A lot of times, yes, it would make little if any difference how you proceed. Sometimes though, it might. Look through the information provided about the submission and decide for yourself how you wish to proceed.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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